Re: More on information, meaning, and biological application

Glenn R. Morton (
Mon, 29 Jun 1998 20:39:58 -0500

At 02:22 PM 6/29/98 -0700, Greg Billock wrote:
>The difference between information as defined for communications systems
>purposes in the Shannon theory and colloquial uses cause some problems,
>but these have very real effects on attempted applications of info
>theory to genetics.
>In the Shannon theory, information is divorced from meaning, and is related
>exclusively to the resolution of uncertainty regarding the message
>(i.e. integrating -p log p over the distribution of possible incoming
>messages). Shannon theorems are limit theorems regarding channels, how
>much information you can stuff through them, and assumes you will
>have a great deal of freedom in codeword assignment. That's why the
>theory works so well even though it ignores meaning--the meaning can
>be taken out of the system more-or-less arbitrarily by the users (the
>source and sink), and doesn't depend upon the transmission system.
>In applying this to genetics, there is an initial problem of figuring
>out (in order to use the Shannon framework) what exactly the messages
>are which are to be expected, and thus how much information is stored
>in the genome, and where.

Whoa! Aren't you now using the word 'message' in place of 'information' or
'semantic meaning'? The DNA consists of both coding and non-coding
regions. But as far as information is concerned, it is the entire sequence
which calculates the information (in the mathematical sense) content, that
is, coding plus noncoding regions.

>The problem is that this distribution is
>intimately tied up with a very meaning-full process: survival on
>Planet Earth. We can be absolutely sure that no species of bird will
>turn out to have genomes which code for methane metabolism, so a vast
>number of possible genomes is ruled out of consideration. But the
>reason we rule it out is because of environmental constraints on the
>planet which we didn't choose, the birds didn't choose, and neither of
>us can control. We don't have the freedom to live with whatever
>genome we like--constraints relating to the 'meaning' of the 'message'
>of our genomes (decoded into proteins) are very strict. As we all
>appreciate, it doesn't take much genomically awry to cause some
>much-less-viable organisms. This means we're on a relatively smaller
>territory in genome-space, and the information required to resolve
>*exactly* where we are is much less.

No we can't live anywhere in genome space but there as you said, meaning is
outside of information theory and as Yockey points out specificity is also
outside of information theory, just like meaning is outside of information
theory. specificity (the ability of a molecule to perform a particular
function like create a life form) is the molecular equivalent of 'meaning'.

"Each message can be assigned a meaning or specificity and thus carries
information, knowledge or intelligence. H reflects the character of the
probability distribution pI . A broad distribution provides a maximum
choice at the source or uncertainty at the receiver. H is a maximum if all
p[I]= 1/n." ~ H. P. Yockey, "An Application of Information Theory to the
Central Dogma and the Sequence Hypothesis," Journal of Theoretical Biology,
46(1974):369-406, p. 373
>This is a point Gould often highlights--much less evolution may be
>due to natural selection than we thought, because it could be that
>the path species are travelling in this much-reduced genomic territory
>is more like a 'one-way street' than a network of roads in a
>large subdivision.

I would agree with this


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